Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Protein secondary structure prediction using local alignments

A A Salamov1, V V Solovyev

  • 1Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA.

Journal of Molecular Biology
|April 25, 1997
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Section-level genome sequencing and comparative genomics of <i>Aspergillus</i> sections <i>Cavernicolus</i> and <i>Usti</i>.

Studies in mycology·2025
Same author

T-Cell Engagers Based Bioassay for Evaluation of PD-1/PD-L1 Inhibitors Activity.

Biochemistry. Biokhimiia·2019
Same author

Hydroxycobalamin catalyzes the oxidation of diethyldithiocarbamate and increases its cytotoxicity independently of copper ions.

Redox biology·2018
Same author

Author Correction: Long-range non-diffusive spin transfer in a Hall insulator.

Scientific reports·2018
Same author

Long-range non-diffusive spin transfer in a Hall insulator.

Scientific reports·2018
Same author

Laser-synthesized oxide-passivated bright Si quantum dots for bioimaging.

Scientific reports·2016
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

This study introduces a novel nearest-neighbor method for protein secondary structure prediction, achieving high accuracy using single sequences. This approach is particularly effective for proteins lacking known homologs, advancing structural biology research.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Accurate protein secondary structure prediction is crucial for understanding protein function and structure.
  • Existing methods often rely on multiple sequence alignments, limiting their application to proteins with known homologs.

Purpose of the Study:

  • To develop a novel nearest-neighbor algorithm for secondary structure prediction that utilizes single query sequences.
  • To achieve high prediction accuracy, especially for proteins without known homologous sequences.

Main Methods:

  • A variant of the nearest-neighbor approach was developed.
  • Computed 50 best non-intersecting local alignments of the query sequence against a database of proteins with known 3D structures.
  • Secondary structure prediction was based on the maximal total score of aligned positions (alpha-helical, beta-strand, or coil states).

Related Experiment Videos

Main Results:

  • The method achieved 71.2% overall three-state accuracy on a benchmark dataset of 124 non-homologous proteins.
  • Verified accuracy of 71.0% on an additional test set of 461 non-homologous proteins.
  • Achieved 73.5% accuracy when using multiple sequence alignments as input.

Conclusions:

  • The developed method offers high prediction accuracy for protein secondary structure, even with single sequences.
  • This approach significantly benefits the prediction of structures for proteins without known homologs.
  • The SSPAL method is accessible via a World Wide Web server.